I have lost (all) thousands of my recon units from my Bunker, they just disappeared.

Sir..Sometimes all you have to do is refresh the game and units will reappear...If you have done this and units are still not there, check your occupies, or reinforcements as sometimes they will get sent to those areas undetected at first..If all fails then please contact Support..Support has the technology to access your game activity and will be able to identify any problems